Using NEURON's Channel Builder

This collection of tutorials shows how to use NEURON's Channel Builder. The Channel Builder is a GUI tool for creating voltage- and ligand-gated channels whose state transitions are described by kinetic schemes and/or HH-style differential equations. Channel gating can be deterministic or stochastic.

Deterministic gating models are based on the (often tacit) assumption of a very large number of channels, each having a very small conductance. This is also called the "continuous system approximation to a large population of channels with discrete states." The result is a simulation in which gating variables, ionic conductances and ionic currents are continuous functions of time. The classical Hodgkin-Huxley model is a typical example of a deterministic gating model.
Stochastic gating models assume random, independent state transitions of countably many channels. Simulations show abrupt changes of gating variables, ionic conductances, and ionic currents.

The look and feel of this native hoc implementation are very similar to Robert Cannon's Java-based Catacomb Channel Builder, which has been available in NEURON for the past few years. Difficulties of installing the large Java runtime system have so far prevented the general use of Java for critical tools that require 100% availability on all machines.

The present implementation of the Channel Builder is not a complete replacement for NMODL for several reasons (e.g. the Channel Builder is restricted to channels and cannot describe pumps or diffusion). However, it is a very convenient way to add new active currents to NEURON. A configured Channel Builder can export a human-readable, plain text specification of the mechanism. Channels constructed with this tool are available immediately to hoc and NEURON's GUI tools, like any other distributed mechanism or point processes. However, they do not need to be compiled, and they execute slightly faster than equivalent mechanisms created with NMODL.

The Tutorials

Creating a channel from an HH-style specification
Given an HH-style channel specification, we add a new voltage-gated current to NEURON. This introduces material that will be helpful in the "kinetic scheme" tutorial.

Creating a channel from a kinetic scheme specification
Given a kinetic scheme channel specification, we add a new voltage-gated current to NEURON.

Creating a channel with stochastic gating
Given a Channel Builder that implements a deterministic channel specified by a kinetic scheme, we create a new one that implements stochastic gating.

This link will get you a pkzipped collection of these html files and images.

Copyright © 2008 by N.T. Carnevale and M.L. Hines, All Rights Reserved.